How can I restore deleted users in AD after migrating to Microsoft 365?

You can recover from this, but it might be a bit of a hassle. Since your AD recycle bin isn't enabled and your only backup seems to be from a VMware snapshot, I suggest you delete the affected accounts in Azure and then recreate them in AD. After that, let the accounts sync back to Azure. If you want to keep the mailbox data, make sure to export that before making any changes, then restore it to the new user accounts afterward. Also, consider enabling the AD recycle bin and setting up a proper backup system for future safety.

If you don’t have the AD Recycle Bin enabled, you might still recover some data, but you'll have to recreate some settings manually. There's a hidden "Deleted Objects" container accessible through ADSI Edit. But be cautious with this method unless you're very familiar with what you're doing.

If your goal is to fully move away from on-premises Exchange, consider updating your DNS records to point to Microsoft 365 and change the settings under mail flow in Exchange to make your domain authoritative. This way, you can still manage your users on-prem but rely solely on Microsoft 365 for email flow, meaning the missing accounts in on-prem Exchange won't disrupt incoming mail.

Do you have the AD recycle bin enabled? If you do, you could easily restore those users from there. Unfortunately, if it's disabled, then you're in a bit of a bind.

I'm curious about how those users are still showing up in the cloud if your sync tool isn't working. The easiest route would be to restore the AD users; the sync should fix the issue. But if you can't restore and have to create new users manually, try to match the GUIDs for the users you had.